Variant report

Variant	rs9849280
Chromosome Location	chr3:48576897-48576898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48575329..48579039-chr3:48581677..48584572,3	K562	blood:
2	chr3:48575329..48578020-chr3:48582630..48584572,2	K562	blood:
3	chr3:48571448..48573714-chr3:48576001..48578662,2	MCF-7	breast:
4	chr3:48576844..48579283-chr3:48584714..48587682,3	MCF-7	breast:
5	chr3:48540872..48542746-chr3:48576018..48578819,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114268	Chromatin interaction
ENSG00000164054	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10049154	0.82[ASN][1000 genomes]
rs10470687	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13060933	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13062576	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13064619	0.82[ASN][1000 genomes]
rs13091944	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13094578	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13100178	0.86[ASN][1000 genomes]
rs13319635	0.94[ASN][1000 genomes]
rs13319651	0.94[ASN][1000 genomes]
rs2006871	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2854394	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854395	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28563843	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581474	0.86[ASN][1000 genomes]
rs28881595	0.81[ASN][1000 genomes]
rs35343040	0.80[ASN][1000 genomes]
rs35562294	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3755819	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3969942	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4075082	0.86[ASN][1000 genomes]
rs6442127	0.85[ASN][1000 genomes]
rs6765317	0.80[ASN][1000 genomes]
rs6781283	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6785845	0.82[ASN][1000 genomes]
rs6792156	0.82[ASN][1000 genomes]
rs6792525	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806059	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809981	0.82[ASN][1000 genomes]
rs7428949	0.86[ASN][1000 genomes]
rs7434077	0.86[ASN][1000 genomes]
rs7434107	0.86[ASN][1000 genomes]
rs7623614	0.86[ASN][1000 genomes]
rs7640031	0.86[ASN][1000 genomes]
rs7644771	0.86[ASN][1000 genomes]
rs9810549	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810991	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816942	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9822677	0.82[ASN][1000 genomes]
rs9830581	0.80[ASN][1000 genomes]
rs9835827	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9835902	0.85[ASN][1000 genomes]
rs9837687	1.00[ASN][1000 genomes]
rs9843316	0.80[ASN][1000 genomes]
rs9848824	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850102	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9851743	0.86[ASN][1000 genomes]
rs9851771	0.86[ASN][1000 genomes]
rs9864729	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869698	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871180	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9871608	0.86[ASN][1000 genomes]
rs9878950	0.94[ASN][1000 genomes]
rs9881877	0.92[ASN][1000 genomes]
rs9882962	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48555200-48582200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:48555400-48578000	Strong transcription	HepG2	liver
4	chr3:48556200-48580400	Weak transcription	HSMMtube	muscle
5	chr3:48556200-48586800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:48556400-48586400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:48559600-48586400	Weak transcription	Primary B cells from cord blood	blood
8	chr3:48560600-48578200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:48560800-48577800	Strong transcription	GM12878-XiMat	blood
10	chr3:48561000-48578200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:48562600-48592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:48565800-48583600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:48568000-48577200	Strong transcription	Placenta	Placenta
14	chr3:48568800-48586000	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:48569000-48579200	Weak transcription	Thymus	Thymus
16	chr3:48569200-48578000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:48569800-48577600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:48569800-48578200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:48570000-48578000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:48570000-48578000	Strong transcription	Brain Germinal Matrix	brain
21	chr3:48570000-48578000	Strong transcription	Fetal Brain Female	brain
22	chr3:48570000-48578000	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr3:48570400-48577800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:48570400-48580600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:48570600-48591600	Weak transcription	Fetal Brain Male	brain
26	chr3:48571000-48578200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:48571000-48581800	Strong transcription	Fetal Intestine Small	intestine
28	chr3:48571200-48578000	Strong transcription	Fetal Stomach	stomach
29	chr3:48571400-48577600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:48571400-48577600	Strong transcription	Brain Hippocampus Middle	brain
31	chr3:48571400-48577600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:48571400-48578000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:48571400-48580600	Weak transcription	Left Ventricle	heart
34	chr3:48571800-48577200	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr3:48571800-48577600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:48571800-48578000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:48571800-48579400	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:48572000-48577200	Strong transcription	Ovary	ovary
39	chr3:48572000-48579600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:48572200-48583800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:48572400-48577600	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:48572400-48578000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr3:48572600-48577000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:48572600-48577000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:48572600-48577200	Strong transcription	Brain Cingulate Gyrus	brain
46	chr3:48572600-48578000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:48572600-48578000	Strong transcription	Fetal Intestine Large	intestine
48	chr3:48572600-48579400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:48572600-48579800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:48572600-48581800	Strong transcription	H9 Cell Line	embryonic stem cell

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